Difficulty: Introductory to Intermediate | Prerequisites: General Chemistry (CHEM 1062/1066 or equivalent)
These four chapters lay the groundwork for everything else in organic chemistry. You learn how atoms bond and why molecular shape matters (Ch. 1), how to name and draw the simplest hydrocarbons (Ch. 2), how those molecules twist and flex in three dimensions (Ch. 3), and how mirror-image molecules can behave completely differently in biological systems (Ch. 4). If you can read a Lewis structure, assign hybridisation, and identify a chiral centre by the end of this block, you are set for the rest of the course.
Electronegativity
A measure of how strongly an atom attracts shared electrons in a covalent bond. In simple terms, the higher the electronegativity, the more that atom hogs the electron density.
Lewis structure
A diagram showing all valence electrons in a molecule as bonding pairs (lines) and lone pairs (dots). Think of it as the molecular blueprint that tells you where every electron lives.
Formal charge
The charge assigned to an atom in a Lewis structure when electrons are divided equally between bonded atoms. Calculated as: valence electrons minus (lone pair electrons + half of bonding electrons).
Hybridisation (sp3, sp2, sp)
The mixing of atomic orbitals to form new, equivalent hybrid orbitals. sp3 gives tetrahedral geometry (109.5 degrees), sp2 gives trigonal planar (120 degrees), and sp gives linear (180 degrees). In simple terms, hybridisation tells you the shape around any given atom.
Constitutional isomers (structural isomers)
Molecules with the same molecular formula but different connectivity of atoms. Think of these as different arrangements of the same LEGO bricks.
Conformations
Different spatial arrangements of atoms that result from rotation around single bonds. These are not different molecules, just different poses of the same molecule.
Staggered conformation
A conformation in which bonds on adjacent carbons are as far apart as possible (60 degrees apart in a Newman projection). This is the lower-energy arrangement.
Eclipsed conformation
A conformation in which bonds on adjacent carbons line up directly behind one another (0 degrees apart in a Newman projection). This is the higher-energy arrangement due to torsional strain.
Newman projection
A way of drawing a molecule looking straight down a carbon-carbon bond. The front carbon is a dot, the back carbon is a circle. Lets you see conformational relationships at a glance.
Gauche interaction
The steric strain that occurs when two large groups are 60 degrees apart in a Newman projection. Costs roughly 3.8 kJ/mol for two methyl groups.
Anti conformation
The most stable staggered conformation, where the two largest substituents are 180 degrees apart in a Newman projection.
Torsional strain
The resistance to rotation about a bond caused by repulsion between bonding electrons on adjacent atoms. In simple terms, eclipsed bonds push against each other.
Angle strain (Baeyer strain)
The strain in a molecule caused by bond angles deviating from the ideal values. This is why cyclopropane (60 degree angles vs. the ideal 109.5 degrees) is so reactive.
Axial and equatorial positions
The two types of bond positions on a cyclohexane chair. Axial bonds point straight up or down; equatorial bonds point roughly sideways. Large substituents prefer equatorial because of 1,3-diaxial interactions.
1,3-diaxial interaction
The steric strain between an axial substituent and the axial hydrogens two carbons away on the same side of a cyclohexane ring. This is the main reason large groups prefer equatorial positions.
Chirality
The property of a molecule that makes it non-superimposable on its mirror image. In simple terms, your hands are chiral: left and right are mirror images, but you cannot perfectly stack one on top of the other.
Chiral centre (stereogenic centre, stereocentre)
A carbon atom bonded to four different substituents. This is the most common source of chirality in organic molecules.
Enantiomers
A pair of molecules that are non-superimposable mirror images of each other. They have identical physical properties (boiling point, melting point) except for the direction they rotate plane-polarised light.
Diastereomers
Stereoisomers that are not mirror images of each other. Unlike enantiomers, diastereomers have different physical properties.
Meso compound
A molecule that contains chiral centres but is achiral overall because it has an internal plane of symmetry. The chirality of one centre cancels out the other.
R and S configuration (Cahn-Ingold-Prelog rules)
The system used to assign absolute configuration at a chiral centre. Substituents are ranked by atomic number, and the arrangement (clockwise = R, anticlockwise = S) is read with the lowest-priority group pointing away from you.
Optical activity
The ability of a chiral substance to rotate the plane of plane-polarised light. Measured with a polarimeter. Clockwise rotation = dextrorotatory (+); anticlockwise = levorotatory (-).
Specific rotation [alpha]
The standardised measure of optical activity, calculated as observed rotation divided by (path length in dm times concentration in g/mL). A physical constant for a given compound at a given temperature and wavelength.
Racemic mixture (racemate)
A 50:50 mixture of two enantiomers. Shows zero net optical rotation because the rotations cancel out.
Organic chemistry is the chemistry of carbon compounds. Carbon is uniquely suited to forming the backbone of complex molecules because it forms four strong covalent bonds and can bond to itself indefinitely.
Electron configuration determines bonding behaviour. Carbon's ground state (1s2 2s2 2p2) does not explain four equivalent bonds; hybridisation does.
Atomic orbitals (s, p) combine to form hybrid orbitals:
sp3: four equivalent orbitals, tetrahedral, 109.5 degree bond angles (e.g. methane)
sp2: three equivalent orbitals in a plane, 120 degrees, with one unhybridised p orbital perpendicular to the plane (e.g. ethene)
sp: two orbitals at 180 degrees, two unhybridised p orbitals (e.g. ethyne)
Covalent bonds form by sharing electrons. A single bond is one sigma bond; a double bond is one sigma plus one pi; a triple bond is one sigma plus two pi.
Sigma bonds have electron density along the bond axis. Pi bonds have electron density above and below the bond axis. Pi bonds are weaker than sigma bonds and more reactive.
Polar covalent bonds arise when atoms of different electronegativity share electrons unequally. The dipole moment depends on both the magnitude of the charge difference and the bond length.
Electronegativity increases across a period (left to right) and up a group in the periodic table. Oxygen and nitrogen are the most common electronegative atoms in organic molecules.
Drawing Lewis structures: count total valence electrons, connect atoms with single bonds, complete octets on outer atoms, place remaining electrons on the central atom, and convert lone pairs to bonds if the central atom lacks an octet.
Formal charge = (valence electrons) minus (lone pair electrons) minus (half of bonding electrons). Structures with the fewest formal charges are preferred. Negative formal charges should sit on the more electronegative atom.
Resonance structures are different Lewis structures for the same molecule that differ only in electron placement, never atom placement.
The real structure is a weighted average (hybrid) of all contributing resonance structures.
Rules for evaluating resonance contributors:
Structures with more covalent bonds are more stable
Structures with fewer formal charges are more stable
Structures with negative charge on the more electronegative atom are more stable
All atoms should have octets where possible (especially C, N, O)
Bronsted-Lowry: acids donate protons, bases accept protons.
Lewis: acids accept electron pairs, bases donate electron pairs. Lewis acid/base theory is broader and more useful in organic chemistry.
pKa is the negative log of the acid dissociation constant. Lower pKa = stronger acid. A difference of one pKa unit means a tenfold difference in acidity.
Factors affecting acidity:
Element effect: acidity increases across a period (C-H < N-H < O-H < F-H) and down a group (H-F < H-Cl < H-Br < H-I)
Inductive effects: electron-withdrawing groups stabilise the conjugate base and increase acidity
Resonance: delocalisation of the negative charge in the conjugate base increases acidity (e.g. carboxylic acids vs. alcohols)
Hybridisation: s character increases acidity (sp C-H > sp2 C-H > sp3 C-H) because s orbitals hold electrons closer to the nucleus
Find the longest continuous carbon chain: that is the parent name.
Number the chain from the end that gives the lowest locants to substituents.
Name each substituent (methyl, ethyl, propyl, etc.) with its position number.
List substituents alphabetically. Use di-, tri-, tetra- for repeated substituents (these prefixes do not affect alphabetical order).
Common names you should know: isopropyl, isobutyl, sec-butyl, tert-butyl, neopentyl.
Nonpolar molecules: only London dispersion forces (van der Waals forces) hold them together.
Boiling points increase with molecular weight and surface area. Branching lowers boiling point because it reduces surface area.
Alkanes are insoluble in water ("like dissolves like") and less dense than water.
Alkanes are relatively unreactive. Their main reactions are combustion and halogenation (free-radical substitution, covered later).
General formula CnH2n (two fewer hydrogens than the corresponding alkane, because forming the ring uses one degree of unsaturation).
Named by adding "cyclo-" before the alkane name. Substituents are numbered to give the lowest possible locants.
Ring strain: the deviation of bond angles from ideal values. Cyclopropane (60 degrees) and cyclobutane (90 degrees) have significant angle strain. Cyclopentane has slight strain. Cyclohexane is nearly strain-free because it adopts a non-planar chair conformation.
The chair conformation is the most stable form of cyclohexane. It eliminates both angle strain and torsional strain.
Each carbon in the chair has one axial bond (pointing up or down, perpendicular to the rough plane of the ring) and one equatorial bond (pointing roughly outward).
Ring flip: cyclohexane can interconvert between two chair conformations. During a ring flip, all axial positions become equatorial and all equatorial become axial.
Substituents prefer equatorial positions to avoid 1,3-diaxial interactions. The larger the substituent, the stronger this preference. For tert-butyl, the equatorial preference is so large that it essentially locks the ring.
The energy difference between axial and equatorial conformations is called the A-value (conformational free energy). Larger A-values mean stronger equatorial preference.
Formula: degrees of unsaturation = (2C + 2 + N - H - X) / 2, where C = carbons, N = nitrogens, H = hydrogens, X = halogens.
Each degree of unsaturation represents either one ring or one pi bond. A triple bond counts as two degrees.
This is a quick diagnostic: if a formula gives zero degrees of unsaturation, the molecule must be a saturated, acyclic compound.
Rotation about the C-C single bond in ethane produces an infinite number of conformations, but two extremes matter: staggered (all bonds 60 degrees apart, energy minimum) and eclipsed (all bonds aligned, energy maximum).
The energy barrier to rotation is about 12 kJ/mol, which is low enough that rotation is essentially free at room temperature. Ethane does not exist in a single conformation; it constantly rotates.
Torsional strain in the eclipsed conformation comes from repulsion between bonding electrons on adjacent carbons.
Butane introduces steric strain alongside torsional strain, because the two methyl groups can interact.
The four key conformations along the C2-C3 bond (viewed as a Newman projection):
Anti: methyl groups 180 degrees apart. Lowest energy.
Gauche: methyl groups 60 degrees apart. About 3.8 kJ/mol higher than anti.
Eclipsed (methyl-H): about 16 kJ/mol above anti.
Totally eclipsed (methyl-methyl, syn-periplanar): highest energy, about 19 kJ/mol above anti.
At room temperature, butane exists primarily in the anti and gauche conformations, with anti slightly favoured.
Cyclopropane: forced into a planar, equilateral triangle. Maximum angle strain (60 degrees vs. ideal 109.5 degrees) and full eclipsing of all C-H bonds. Very reactive.
Cyclobutane: slightly puckered to reduce eclipsing strain, at the cost of a small increase in angle strain.
Cyclopentane: adopts an envelope conformation (four carbons in a plane, one up) to reduce eclipsing.
Cyclohexane: the chair conformation eliminates both angle strain and eclipsing. The boat conformation is higher in energy due to flagpole interactions and eclipsing; the twist-boat is slightly lower than the boat.
Substituents on a ring can be on the same side (cis) or opposite sides (trans) of the ring plane.
cis and trans isomers of cycloalkanes are diastereomers: they have different physical properties and cannot interconvert without breaking bonds.
In substituted cyclohexanes, cis/trans relationships translate into specific axial/equatorial patterns:
1,2-disubstituted: trans = one axial, one equatorial (in each chair); cis = both axial or both equatorial
1,3-disubstituted: trans = both axial or both equatorial; cis = one axial, one equatorial
1,4-disubstituted: same pattern as 1,2
To determine which chair conformation is more stable, draw both and check which places the larger substituent(s) equatorial.
A molecule is chiral if it cannot be superimposed on its mirror image. The most common cause is a tetrahedral carbon bonded to four different groups (a chiral centre, also called a stereocentre or asymmetric centre).
A molecule with no chiral centres is almost always achiral. A molecule with one chiral centre is always chiral. A molecule with two or more chiral centres may or may not be chiral (it could be a meso compound).
Planes of symmetry: if a molecule has an internal mirror plane, it is achiral regardless of how many chiral centres it has.
The Cahn-Ingold-Prelog priority rules:
Rank the four substituents by atomic number of the atom directly attached to the chiral centre. Higher atomic number = higher priority.
If two substituents start with the same atom, move outward along the chain until you find a point of difference.
Double and triple bonds are treated as if each multiply-bonded atom is duplicated (or triplicated). A C=O is treated as C bonded to (O, O) and O bonded to (C, C).
Orient the molecule so the lowest-priority group (usually H) points away from you. Read the remaining three groups from highest to lowest priority: clockwise = R, anticlockwise = S.
Chiral molecules rotate plane-polarised light. The direction and magnitude of rotation cannot be predicted from R/S configuration; it must be measured experimentally.
Specific rotation [alpha] = observed rotation / (path length in dm x concentration in g/mL). This is a physical constant for a given compound.
A racemic mixture (equal amounts of both enantiomers) shows zero optical rotation.
Enantiomeric excess (ee) = percentage of the major enantiomer minus percentage of the minor enantiomer. ee = (observed specific rotation / specific rotation of pure enantiomer) x 100%.
Enantiomers: non-superimposable mirror images. Same physical properties, opposite optical rotations, identical reactivity with achiral reagents, different reactivity with chiral reagents (this is why chirality matters in biology).
Diastereomers: stereoisomers that are not mirror images. Different physical properties, different reactivities. Can be separated by ordinary physical methods (distillation, crystallisation, chromatography).
Meso compounds: contain chiral centres but have an internal plane of symmetry, making the molecule achiral overall. A meso compound and its "mirror image" are the same molecule.
A way to draw chiral centres on paper. The horizontal bonds project toward you; the vertical bonds project away.
Rules: you may rotate a Fischer projection 180 degrees in the plane (same enantiomer), but rotating 90 degrees gives the opposite enantiomer. Swapping any two groups gives the opposite enantiomer; swapping two groups twice returns you to the original.
Enzymes and receptors are chiral, so they interact differently with different enantiomers of the same compound.
One enantiomer of a drug may be therapeutic while the other is inactive or harmful (the most cited example is thalidomide).
Amino acids in proteins are almost exclusively the L configuration. Sugars in DNA are D configuration. Biology is built on single-enantiomer chemistry.
Formal charge
Formal charge = (valence electrons) - (lone pair electrons) - (1/2 bonding electrons)
Degrees of unsaturation (index of hydrogen deficiency)
DoU = (2C + 2 + N - H - X) / 2
Where C = number of carbons, N = number of nitrogens, H = number of hydrogens, X = number of halogens. Oxygen and sulfur are ignored in the formula.
Specific rotation
[alpha] = alpha(observed) / (l x c)
Where l = path length in decimetres and c = concentration in g/mL.
Enantiomeric excess
ee (%) = |alpha| / |alpha| x 100
Key diagrams to practise drawing
Newman projections of ethane, butane (anti, gauche, eclipsed, totally eclipsed)
Cyclohexane chair conformations with axial and equatorial bonds labelled
Ring flip of a substituted cyclohexane showing axial-to-equatorial interconversion
Fischer projections of simple chiral molecules
Energy diagrams for ethane and butane rotation (dihedral angle vs. potential energy)
Chirality is not an abstract concept. Pharmaceutical companies spend billions ensuring they produce the correct enantiomer of a drug, because the wrong one can be ineffective or dangerous. Ibuprofen, for example, is sold as a racemic mixture, but only the S-enantiomer is the active painkiller; the R-enantiomer is slowly converted to the S form in the body.
Conformational analysis matters in materials science and polymer chemistry. The stiffness or flexibility of a polymer chain depends on the rotational barriers around its backbone bonds, the same energy profiles you study in butane and cyclohexane.
Students often think that constitutional isomers and stereoisomers are the same thing. They are not. Constitutional isomers differ in connectivity (which atoms are bonded to which). Stereoisomers have the same connectivity but differ in spatial arrangement.
Students frequently confuse conformations with configurations. Conformations interconvert by rotation around single bonds (no bond breaking). Configurations (R vs. S, cis vs. trans) require bond breaking to interconvert.
A common mistake is assuming that R configuration = dextrorotatory (+) and S configuration = levorotatory (-). There is no correlation. R/S is an assignment rule based on priority; (+)/(-) is an experimental measurement.
Students often forget that a meso compound is achiral despite having chiral centres. If you see an internal mirror plane, the molecule is achiral, full stop.
⚠️ Drawing Newman projections accurately is a near-certain exam question. Practise until you can draw all conformations of butane from memory and rank them by energy.
⚠️ Chair conformations of cyclohexane, including ring flips with substituents, appear on virtually every Exam 1. Know which chair is more stable and why.
⚠️ Assigning R/S configuration using Cahn-Ingold-Prelog rules is heavily tested. The most common error is forgetting to orient the lowest-priority group away from you before reading clockwise/anticlockwise.
⚠️ Be able to identify the relationship between any pair of molecules: identical, enantiomers, diastereomers, constitutional isomers, or not isomers at all.
⚠️ Formal charge calculation and resonance structure evaluation are fundamental skills tested throughout the course, not just on Exam 1.
⚠️ Acid-base chemistry (pKa, factors affecting acidity) will reappear in nearly every subsequent chapter. Master it now.
True or false: A molecule with two chiral centres must be chiral. (False: it could be a meso compound.)
Fill in the blank: In a Newman projection, the ______ conformation of butane has the two methyl groups 180 degrees apart. (Anti)
True or false: sp2-hybridised carbons have bond angles of approximately 109.5 degrees. (False: 120 degrees.)
Fill in the blank: The formula for degrees of unsaturation is DoU = ______. ((2C + 2 + N - H - X) / 2)
True or false: Enantiomers have different melting points. (False: enantiomers have identical physical properties except for the direction of optical rotation.)
Q: Draw Newman projections for all staggered and eclipsed conformations of butane looking down the C2-C3 bond. Rank them in order of increasing energy.
A: Anti (lowest) < gauche < eclipsed (methyl-H) < totally eclipsed (methyl-methyl, highest). The anti conformation has the two methyl groups 180 degrees apart. Each gauche conformation has them 60 degrees apart. The energy differences are approximately: anti to gauche +3.8 kJ/mol; gauche to eclipsed (methyl-H) +12 kJ/mol; eclipsed (methyl-H) to totally eclipsed +3 kJ/mol.
Q: Assign R or S configuration to (2-bromobutane) where the bromine is on carbon 2 with the hydrogen pointing toward you.
A: First assign priorities: Br (35) > CH2CH3 (C with C,H,H next) > CH3 (C with H,H,H) > H (1). Orient so H points away. Read Br to CH2CH3 to CH3: if clockwise, R; if anticlockwise, S. Always reorient so the lowest-priority group is in the back before reading.
Q: trans-1,4-dimethylcyclohexane has two chair conformations. Draw both and identify which is more stable.
A: In trans-1,4-disubstituted cyclohexane, both substituents are either both equatorial or both axial. The diequatorial chair is more stable because it avoids 1,3-diaxial interactions for both methyl groups.
Q: A compound has the molecular formula C5H8. How many degrees of unsaturation does it have? What structural features could account for this?
A: DoU = (2(5) + 2 - 8) / 2 = 2. This could be two double bonds, one triple bond, two rings, or one ring plus one double bond.
Q: Explain why acetic acid (pKa approximately 4.75) is a much stronger acid than ethanol (pKa approximately 16).
A: The conjugate base of acetic acid (acetate) is stabilised by resonance: the negative charge is delocalised over two equivalent oxygen atoms. The conjugate base of ethanol (ethoxide) has no such resonance stabilisation, so it is a much stronger base and ethanol is correspondingly a weaker acid.
The acid-base concepts from Chapter 1 are the single most reused idea in this course. Every reaction mechanism you study later (nucleophilic substitution, elimination, addition) is, at its core, an electron-pair donor meeting an electron-pair acceptor. Get comfortable with Lewis acids and bases now.
Conformational analysis and chirality feed directly into Chapters 5-8. When you study nucleophilic substitution (SN2), the stereochemistry of the reaction (inversion at the chiral centre) only makes sense if you understand what a chiral centre is and how to track its configuration. When you study elimination reactions, the geometry of the transition state depends on whether substituents are anti-periplanar, a conformational concept.
The naming conventions (IUPAC nomenclature) from Chapter 2 are used for every class of compound going forward. Invest time now so you are not struggling with names while also trying to learn new reactions.
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